Identification of genes related to salt stress tolerance using intron-length polymorphic markers, association mapping and virus-induced gene silencing in cotton

Abstract

Intron length polymorphisms (ILPs), a type of gene-based functional marker, could themselves be related to the particular traits. Here, we developed a genome-wide cotton ILPs based on orthologs annotation from two sequenced diploid species, A-genome Gossypium arboreum and D-genome G. raimondii. We identified 10,180 putative ILP markers from 5,021 orthologous genes. Among these, 535 ILP markers from 9 gene families related to stress were selected for experimental verification. Polymorphic rates were 72.71% between G. arboreum and G. raimondii and 36.45% between G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. Furthermore, 14 polymorphic ILP markers were detected in 264 G. hirsutum accessions. Coupled with previous simple sequence repeats (SSRs) evaluations and salt tolerance assays from the same individuals, we found a total of 25 marker-trait associations involved in nine ILPs. The nine genes, temporally named as C1 to C9, showed the various expressions in different organs and tissues, and five genes (C3, C4, C5, C7 and C9) were significantly upregulated after salt treatment. We verified that the five genes play important roles in salt tolerance. Particularly, silencing of C4 (encodes WRKY DNA-binding protein) and C9 (encodes Mitogen-activated protein kinase) can significantly enhance cotton susceptibility to salt stress.

Assessment of Genetic Diversity in Differently Colored Raspberry Cultivars Using SSR Markers Located in Flavonoid Biosynthesis Genes

“…Significantly higher variation was observed also for SNPs in noncoding regions compared to coding ones [42]. In general, introns are more variable than exons, as they are under less selection pressure during the evolutionary process [43].…”

Identification of SNPs and Candidate Genes Associated With Salt Tolerance at the Seedling Stage in Cotton (Gossypium hirsutum L.)

“… Jia et al (2014a) only detected three SSR markers associated with salt tolerance in MLM using 106 SSRs in 323 G. hirsutum germplasms. Cai et al (2017) found 9 intron length polymorphisms (ILPs) markers for 10 salt stress traits with 535 ILP markers in 264 G. hirsutum accessions. In this study, 713 upland cotton accessions were used to conduct a GWAS of two salt-tolerance related traits with 10,511 SNPs, and we identified 10 and 15 loci for RSR and STL, respectively, of which two common SNP loci (i46598Gh and i47388Gh) on D09 were significantly associated with the two traits.…”

“…A salt-tolerant cultivar (Suwu77-702) and a salt-sensitive cultivar (Shann424) were selected to grow for 7 days in a germination box, and then moved into 1/2 Hogland nutrient solution until the three-true-leaf period (about another 14 days). Under 200 mmol/L NaCl stress, leaves were sampled at 0, 3, 6, 8, 12, 24, and 48 h for measuring the content of the protein, POD, MDA, and H 2 O 2 ( Liu and Li, 2007 ; Cai et al, 2017 ). Three biological replicates were performed.…”

WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update

“…In the past 12 years the website has been visited more than 12 636 545 times by users in more than 186 countries and regions (as of the end of 2017). WEGO was cited over 1536 times by publications covering research topics focusing on various types of species from Bryum argenteum (Bryophytes) ( 23 ) to Polynoidae (scale worms) ( 24 ) and from Gossypium (cotton) ( 25 ) to Bombus terrestris (bumblebee) ( 26 ). We have also benefitted from a great deal of positive feedback and some very constructive suggestions from users worldwide.…”